Closed aqred1 closed 2 years ago
I have two pdbs with the same number of atoms - they correspond to different proteins. When trying to compute their RMSD, I get the following error:
rmsd = MetricRmsd(mol1, 'protein and name CA') data = rmsd.project(mol2) --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) /tmp/ipykernel_10061/796448951.py in <module> 1 rmsd = MetricRmsd(mol1, 'protein and name CA') ----> 2 data = rmsd.project(mol2) /ahf/colab/lib/python3.7/site-packages/moleculekit/projections/metricrmsd.py in project(self, mol) 109 110 if self._pbc: --> 111 mol.wrap(getMolProp("centersel")) 112 # mol.coords = self._wrapPositions(mol.box, mol.coords, centersel) 113 mol.align( /ahf/colab/lib/python3.7/site-packages/moleculekit/molecule.py in wrap(self, wrapsel, fileBonds, guessBonds) 1511 if np.all(self.box == 0): 1512 raise RuntimeError( -> 1513 "Zero box size detected in `Molecule.box`. Cannot wrap simulation." 1514 ) 1515 RuntimeError: Zero box size detected in `Molecule.box`. Cannot wrap simulation.
Perhaps there's a better way to compute RMSDs. Any help is appreciated.
I just added pbc=False and this worked. Closing the issue.
I have two pdbs with the same number of atoms - they correspond to different proteins. When trying to compute their RMSD, I get the following error:
Perhaps there's a better way to compute RMSDs. Any help is appreciated.